Below you find for each supplied fasta file an individual tab. Each tab contains all the results and explanations to help you identify the possible phages.
The results are also grouped by blue tabs. All the citations can be found in the results directory as a .bib file
Fig.1: UpSetR plot summarizes each tool’s performance. Additionally, it shows which tools (black dots) identified the same contigs (black bars).
The “UpSet” plot is an alternative but more detailed Venn diagram, and it summarizes the prediction performance of each tool for your sample.
The total amount of identified phage-contigs per tool is shown in blue bars on the left.
Black bars visualize the number of contigs that each tool or tool combination has uniquely identified, and each tool combination is shown below each black bar as a dot matrix. E.g., a black bar with two dots below it means that these two tools identified the same contigs as phages.
Tab.1: Gene annotation of contigs based on Hmmer and Prodigal, using this database
| contig | prediction_value | predicted_organism_name |
|---|
ctg1_len=102949 0.53 gi_265524965_gb_GU071091.1___Enterobacteria__phage__T7,__complete__genome
Tab. 1: Interactive phage prediction table. The scores/p-values of each column can be filtered. The adjusted table can be exported as a .csv, .pdf or .excel.
WtP uses several phage prediction tools that work differently and generate different outputs. Contigs with the overall highest p-values/scores are displayed at the top, and contigs with low p-values/scores are at the bottom of the table. Each tool’s p-value/score can be individually adjusted and filtered in Table 1. Some tools don’t generate p-values or scores as output, instead they generate categories with likelyhoods, or directly predict and assign the contigs as phage.
The tool’s output and what WtP assigns is shown in the Table below.
Tab.2: The output of each tool and what WtP puts in Tab. 1.
| Tool | Standard output | WtP displayed value |
|---|---|---|
| deepvirfinder | p-value: 0 to 1 | 0 to 1 |
| metaphinder | string: phage | 1 |
| metaphinder own | string: phage | 1 |
| phigaro | score: 0 to 1 | 0 to 1 |
| pprmeta | phage_score: 0 to 1 | 0 to 1 |
| seeker | score: 0 to 1 | 0 to 1 |
| sourmash | similarity: 0 to 1 | 0 to 1 |
| vibrant | prediction: virus | 1 |
| vibrant-virome | prediction: virus | 1 |
| virfinder | p-value: 0 to 1 | 0 to 1 |
| virnet | score: 0 to 1 | 0 to 1 |
| virsorter | category 1, category 2, category 3 | 1, 0.5, 0 |
| virsorter-virome | category 1, category 2, category 3 | 1, 0.5, 0 |
| virsorter2 | dsDNAphage: 0 to 1 | 0 to 1 |
# make sure that the fasta and .csv file are in the same directory
for i in bla ;
hier kommt noch was
oranage: #F79A30
pink #E35E9F
lila #8F2ABF
done
Tab. 1: Taxonomic classification of predicted phages based on sourmash using this database Each column can be filtered. The adjusted table can be exported as a .csv, .pdf or .excel.
hier nochn satz was der wert ist probability
Fig.1: UpSetR plot summarizes each tool’s performance. Additionally, it shows which tools (black dots) identified the same contigs (black bars).
The “UpSet” plot is an alternative but more detailed Venn diagram, and it summarizes the prediction performance of each tool for your sample.
The total amount of identified phage-contigs per tool is shown in blue bars on the left.
Black bars visualize the number of contigs that each tool or tool combination has uniquely identified, and each tool combination is shown below each black bar as a dot matrix. E.g., a black bar with two dots below it means that these two tools identified the same contigs as phages.
Tab.1: Gene annotation of contigs based on Hmmer and Prodigal, using this database
| contig | prediction_value | predicted_organism_name |
|---|
ctg1_len=102949 0.53 gi_265524965_gb_GU071091.1___Enterobacteria__phage__T7,__complete__genome
Tab. 1: Interactive phage prediction table. The scores/p-values of each column can be filtered. The adjusted table can be exported as a .csv, .pdf or .excel.
WtP uses several phage prediction tools that work differently and generate different outputs. Contigs with the overall highest p-values/scores are displayed at the top, and contigs with low p-values/scores are at the bottom of the table. Each tool’s p-value/score can be individually adjusted and filtered in Table 1. Some tools don’t generate p-values or scores as output, instead they generate categories with likelyhoods, or directly predict and assign the contigs as phage.
The tool’s output and what WtP assigns is shown in the Table below.
Tab.2: The output of each tool and what WtP puts in Tab. 1.
| Tool | Standard output | WtP displayed value |
|---|---|---|
| deepvirfinder | p-value: 0 to 1 | 0 to 1 |
| metaphinder | string: phage | 1 |
| metaphinder own | string: phage | 1 |
| phigaro | score: 0 to 1 | 0 to 1 |
| pprmeta | phage_score: 0 to 1 | 0 to 1 |
| seeker | score: 0 to 1 | 0 to 1 |
| sourmash | similarity: 0 to 1 | 0 to 1 |
| vibrant | prediction: virus | 1 |
| vibrant-virome | prediction: virus | 1 |
| virfinder | p-value: 0 to 1 | 0 to 1 |
| virnet | score: 0 to 1 | 0 to 1 |
| virsorter | category 1, category 2, category 3 | 1, 0.5, 0 |
| virsorter-virome | category 1, category 2, category 3 | 1, 0.5, 0 |
| virsorter2 | dsDNAphage: 0 to 1 | 0 to 1 |
# make sure that the fasta and .csv file are in the same directory
for i in bla ;
hier kommt noch was
oranage: #F79A30
pink #E35E9F
lila #8F2ABF
done
Tab. 1: Taxonomic classification of predicted phages based on sourmash using this database Each column can be filtered. The adjusted table can be exported as a .csv, .pdf or .excel.
hier nochn satz was der wert ist probability
Fig.1: UpSetR plot summarizes each tool’s performance. Additionally, it shows which tools (black dots) identified the same contigs (black bars).
The “UpSet” plot is an alternative but more detailed Venn diagram, and it summarizes the prediction performance of each tool for your sample.
The total amount of identified phage-contigs per tool is shown in blue bars on the left.
Black bars visualize the number of contigs that each tool or tool combination has uniquely identified, and each tool combination is shown below each black bar as a dot matrix. E.g., a black bar with two dots below it means that these two tools identified the same contigs as phages.
Tab.1: Gene annotation of contigs based on Hmmer and Prodigal, using this database
| contig | prediction_value | predicted_organism_name |
|---|
ctg1_len=102949 0.53 gi_265524965_gb_GU071091.1___Enterobacteria__phage__T7,__complete__genome
Tab. 1: Interactive phage prediction table. The scores/p-values of each column can be filtered. The adjusted table can be exported as a .csv, .pdf or .excel.
WtP uses several phage prediction tools that work differently and generate different outputs. Contigs with the overall highest p-values/scores are displayed at the top, and contigs with low p-values/scores are at the bottom of the table. Each tool’s p-value/score can be individually adjusted and filtered in Table 1. Some tools don’t generate p-values or scores as output, instead they generate categories with likelyhoods, or directly predict and assign the contigs as phage.
The tool’s output and what WtP assigns is shown in the Table below.
Tab.2: The output of each tool and what WtP puts in Tab. 1.
| Tool | Standard output | WtP displayed value |
|---|---|---|
| deepvirfinder | p-value: 0 to 1 | 0 to 1 |
| metaphinder | string: phage | 1 |
| metaphinder own | string: phage | 1 |
| phigaro | score: 0 to 1 | 0 to 1 |
| pprmeta | phage_score: 0 to 1 | 0 to 1 |
| seeker | score: 0 to 1 | 0 to 1 |
| sourmash | similarity: 0 to 1 | 0 to 1 |
| vibrant | prediction: virus | 1 |
| vibrant-virome | prediction: virus | 1 |
| virfinder | p-value: 0 to 1 | 0 to 1 |
| virnet | score: 0 to 1 | 0 to 1 |
| virsorter | category 1, category 2, category 3 | 1, 0.5, 0 |
| virsorter-virome | category 1, category 2, category 3 | 1, 0.5, 0 |
| virsorter2 | dsDNAphage: 0 to 1 | 0 to 1 |
# make sure that the fasta and .csv file are in the same directory
for i in bla ;
hier kommt noch was
oranage: #F79A30
pink #E35E9F
lila #8F2ABF
done
Tab. 1: Taxonomic classification of predicted phages based on sourmash using this database Each column can be filtered. The adjusted table can be exported as a .csv, .pdf or .excel.
hier nochn satz was der wert ist probability
Fig.1: UpSetR plot summarizes each tool’s performance. Additionally, it shows which tools (black dots) identified the same contigs (black bars).
The “UpSet” plot is an alternative but more detailed Venn diagram, and it summarizes the prediction performance of each tool for your sample.
The total amount of identified phage-contigs per tool is shown in blue bars on the left.
Black bars visualize the number of contigs that each tool or tool combination has uniquely identified, and each tool combination is shown below each black bar as a dot matrix. E.g., a black bar with two dots below it means that these two tools identified the same contigs as phages.
Tab.1: Gene annotation of contigs based on Hmmer and Prodigal, using this database
| contig | prediction_value | predicted_organism_name |
|---|
ctg1_len=102949 0.53 gi_265524965_gb_GU071091.1___Enterobacteria__phage__T7,__complete__genome
Tab. 1: Interactive phage prediction table. The scores/p-values of each column can be filtered. The adjusted table can be exported as a .csv, .pdf or .excel.
WtP uses several phage prediction tools that work differently and generate different outputs. Contigs with the overall highest p-values/scores are displayed at the top, and contigs with low p-values/scores are at the bottom of the table. Each tool’s p-value/score can be individually adjusted and filtered in Table 1. Some tools don’t generate p-values or scores as output, instead they generate categories with likelyhoods, or directly predict and assign the contigs as phage.
The tool’s output and what WtP assigns is shown in the Table below.
Tab.2: The output of each tool and what WtP puts in Tab. 1.
| Tool | Standard output | WtP displayed value |
|---|---|---|
| deepvirfinder | p-value: 0 to 1 | 0 to 1 |
| metaphinder | string: phage | 1 |
| metaphinder own | string: phage | 1 |
| phigaro | score: 0 to 1 | 0 to 1 |
| pprmeta | phage_score: 0 to 1 | 0 to 1 |
| seeker | score: 0 to 1 | 0 to 1 |
| sourmash | similarity: 0 to 1 | 0 to 1 |
| vibrant | prediction: virus | 1 |
| vibrant-virome | prediction: virus | 1 |
| virfinder | p-value: 0 to 1 | 0 to 1 |
| virnet | score: 0 to 1 | 0 to 1 |
| virsorter | category 1, category 2, category 3 | 1, 0.5, 0 |
| virsorter-virome | category 1, category 2, category 3 | 1, 0.5, 0 |
| virsorter2 | dsDNAphage: 0 to 1 | 0 to 1 |
# make sure that the fasta and .csv file are in the same directory
for i in bla ;
hier kommt noch was
oranage: #F79A30
pink #E35E9F
lila #8F2ABF
done
Tab. 1: Taxonomic classification of predicted phages based on sourmash using this database Each column can be filtered. The adjusted table can be exported as a .csv, .pdf or .excel.
hier nochn satz was der wert ist probability
Fig.1: UpSetR plot summarizes each tool’s performance. Additionally, it shows which tools (black dots) identified the same contigs (black bars).
The “UpSet” plot is an alternative but more detailed Venn diagram, and it summarizes the prediction performance of each tool for your sample.
The total amount of identified phage-contigs per tool is shown in blue bars on the left.
Black bars visualize the number of contigs that each tool or tool combination has uniquely identified, and each tool combination is shown below each black bar as a dot matrix. E.g., a black bar with two dots below it means that these two tools identified the same contigs as phages.
Tab.1: Gene annotation of contigs based on Hmmer and Prodigal, using this database
| contig | prediction_value | predicted_organism_name |
|---|
ctg1_len=102949 0.53 gi_265524965_gb_GU071091.1___Enterobacteria__phage__T7,__complete__genome
Tab. 1: Interactive phage prediction table. The scores/p-values of each column can be filtered. The adjusted table can be exported as a .csv, .pdf or .excel.
WtP uses several phage prediction tools that work differently and generate different outputs. Contigs with the overall highest p-values/scores are displayed at the top, and contigs with low p-values/scores are at the bottom of the table. Each tool’s p-value/score can be individually adjusted and filtered in Table 1. Some tools don’t generate p-values or scores as output, instead they generate categories with likelyhoods, or directly predict and assign the contigs as phage.
The tool’s output and what WtP assigns is shown in the Table below.
Tab.2: The output of each tool and what WtP puts in Tab. 1.
| Tool | Standard output | WtP displayed value |
|---|---|---|
| deepvirfinder | p-value: 0 to 1 | 0 to 1 |
| metaphinder | string: phage | 1 |
| metaphinder own | string: phage | 1 |
| phigaro | score: 0 to 1 | 0 to 1 |
| pprmeta | phage_score: 0 to 1 | 0 to 1 |
| seeker | score: 0 to 1 | 0 to 1 |
| sourmash | similarity: 0 to 1 | 0 to 1 |
| vibrant | prediction: virus | 1 |
| vibrant-virome | prediction: virus | 1 |
| virfinder | p-value: 0 to 1 | 0 to 1 |
| virnet | score: 0 to 1 | 0 to 1 |
| virsorter | category 1, category 2, category 3 | 1, 0.5, 0 |
| virsorter-virome | category 1, category 2, category 3 | 1, 0.5, 0 |
| virsorter2 | dsDNAphage: 0 to 1 | 0 to 1 |
# make sure that the fasta and .csv file are in the same directory
for i in bla ;
hier kommt noch was
oranage: #F79A30
pink #E35E9F
lila #8F2ABF
done
Tab. 1: Taxonomic classification of predicted phages based on sourmash using this database Each column can be filtered. The adjusted table can be exported as a .csv, .pdf or .excel.
hier nochn satz was der wert ist probability
Fig.1: UpSetR plot summarizes each tool’s performance. Additionally, it shows which tools (black dots) identified the same contigs (black bars).
The “UpSet” plot is an alternative but more detailed Venn diagram, and it summarizes the prediction performance of each tool for your sample.
The total amount of identified phage-contigs per tool is shown in blue bars on the left.
Black bars visualize the number of contigs that each tool or tool combination has uniquely identified, and each tool combination is shown below each black bar as a dot matrix. E.g., a black bar with two dots below it means that these two tools identified the same contigs as phages.
Tab.1: Gene annotation of contigs based on Hmmer and Prodigal, using this database
| contig | prediction_value | predicted_organism_name |
|---|
ctg1_len=102949 0.53 gi_265524965_gb_GU071091.1___Enterobacteria__phage__T7,__complete__genome
Tab. 1: Interactive phage prediction table. The scores/p-values of each column can be filtered. The adjusted table can be exported as a .csv, .pdf or .excel.
WtP uses several phage prediction tools that work differently and generate different outputs. Contigs with the overall highest p-values/scores are displayed at the top, and contigs with low p-values/scores are at the bottom of the table. Each tool’s p-value/score can be individually adjusted and filtered in Table 1. Some tools don’t generate p-values or scores as output, instead they generate categories with likelyhoods, or directly predict and assign the contigs as phage.
The tool’s output and what WtP assigns is shown in the Table below.
Tab.2: The output of each tool and what WtP puts in Tab. 1.
| Tool | Standard output | WtP displayed value |
|---|---|---|
| deepvirfinder | p-value: 0 to 1 | 0 to 1 |
| metaphinder | string: phage | 1 |
| metaphinder own | string: phage | 1 |
| phigaro | score: 0 to 1 | 0 to 1 |
| pprmeta | phage_score: 0 to 1 | 0 to 1 |
| seeker | score: 0 to 1 | 0 to 1 |
| sourmash | similarity: 0 to 1 | 0 to 1 |
| vibrant | prediction: virus | 1 |
| vibrant-virome | prediction: virus | 1 |
| virfinder | p-value: 0 to 1 | 0 to 1 |
| virnet | score: 0 to 1 | 0 to 1 |
| virsorter | category 1, category 2, category 3 | 1, 0.5, 0 |
| virsorter-virome | category 1, category 2, category 3 | 1, 0.5, 0 |
| virsorter2 | dsDNAphage: 0 to 1 | 0 to 1 |
# make sure that the fasta and .csv file are in the same directory
for i in bla ;
hier kommt noch was
oranage: #F79A30
pink #E35E9F
lila #8F2ABF
done
Tab. 1: Taxonomic classification of predicted phages based on sourmash using this database Each column can be filtered. The adjusted table can be exported as a .csv, .pdf or .excel.
hier nochn satz was der wert ist probability
Fig.1: UpSetR plot summarizes each tool’s performance. Additionally, it shows which tools (black dots) identified the same contigs (black bars).
The “UpSet” plot is an alternative but more detailed Venn diagram, and it summarizes the prediction performance of each tool for your sample.
The total amount of identified phage-contigs per tool is shown in blue bars on the left.
Black bars visualize the number of contigs that each tool or tool combination has uniquely identified, and each tool combination is shown below each black bar as a dot matrix. E.g., a black bar with two dots below it means that these two tools identified the same contigs as phages.
Tab.1: Gene annotation of contigs based on Hmmer and Prodigal, using this database
| contig | prediction_value | predicted_organism_name |
|---|
ctg1_len=102949 0.53 gi_265524965_gb_GU071091.1___Enterobacteria__phage__T7,__complete__genome
Tab. 1: Interactive phage prediction table. The scores/p-values of each column can be filtered. The adjusted table can be exported as a .csv, .pdf or .excel.
WtP uses several phage prediction tools that work differently and generate different outputs. Contigs with the overall highest p-values/scores are displayed at the top, and contigs with low p-values/scores are at the bottom of the table. Each tool’s p-value/score can be individually adjusted and filtered in Table 1. Some tools don’t generate p-values or scores as output, instead they generate categories with likelyhoods, or directly predict and assign the contigs as phage.
The tool’s output and what WtP assigns is shown in the Table below.
Tab.2: The output of each tool and what WtP puts in Tab. 1.
| Tool | Standard output | WtP displayed value |
|---|---|---|
| deepvirfinder | p-value: 0 to 1 | 0 to 1 |
| metaphinder | string: phage | 1 |
| metaphinder own | string: phage | 1 |
| phigaro | score: 0 to 1 | 0 to 1 |
| pprmeta | phage_score: 0 to 1 | 0 to 1 |
| seeker | score: 0 to 1 | 0 to 1 |
| sourmash | similarity: 0 to 1 | 0 to 1 |
| vibrant | prediction: virus | 1 |
| vibrant-virome | prediction: virus | 1 |
| virfinder | p-value: 0 to 1 | 0 to 1 |
| virnet | score: 0 to 1 | 0 to 1 |
| virsorter | category 1, category 2, category 3 | 1, 0.5, 0 |
| virsorter-virome | category 1, category 2, category 3 | 1, 0.5, 0 |
| virsorter2 | dsDNAphage: 0 to 1 | 0 to 1 |
# make sure that the fasta and .csv file are in the same directory
for i in bla ;
hier kommt noch was
oranage: #F79A30
pink #E35E9F
lila #8F2ABF
done
Tab. 1: Taxonomic classification of predicted phages based on sourmash using this database Each column can be filtered. The adjusted table can be exported as a .csv, .pdf or .excel.
hier nochn satz was der wert ist probability
Fig.1: UpSetR plot summarizes each tool’s performance. Additionally, it shows which tools (black dots) identified the same contigs (black bars).
The “UpSet” plot is an alternative but more detailed Venn diagram, and it summarizes the prediction performance of each tool for your sample.
The total amount of identified phage-contigs per tool is shown in blue bars on the left.
Black bars visualize the number of contigs that each tool or tool combination has uniquely identified, and each tool combination is shown below each black bar as a dot matrix. E.g., a black bar with two dots below it means that these two tools identified the same contigs as phages.
Tab.1: Gene annotation of contigs based on Hmmer and Prodigal, using this database
| contig | prediction_value | predicted_organism_name |
|---|
ctg1_len=102949 0.53 gi_265524965_gb_GU071091.1___Enterobacteria__phage__T7,__complete__genome
Tab. 1: Interactive phage prediction table. The scores/p-values of each column can be filtered. The adjusted table can be exported as a .csv, .pdf or .excel.
WtP uses several phage prediction tools that work differently and generate different outputs. Contigs with the overall highest p-values/scores are displayed at the top, and contigs with low p-values/scores are at the bottom of the table. Each tool’s p-value/score can be individually adjusted and filtered in Table 1. Some tools don’t generate p-values or scores as output, instead they generate categories with likelyhoods, or directly predict and assign the contigs as phage.
The tool’s output and what WtP assigns is shown in the Table below.
Tab.2: The output of each tool and what WtP puts in Tab. 1.
| Tool | Standard output | WtP displayed value |
|---|---|---|
| deepvirfinder | p-value: 0 to 1 | 0 to 1 |
| metaphinder | string: phage | 1 |
| metaphinder own | string: phage | 1 |
| phigaro | score: 0 to 1 | 0 to 1 |
| pprmeta | phage_score: 0 to 1 | 0 to 1 |
| seeker | score: 0 to 1 | 0 to 1 |
| sourmash | similarity: 0 to 1 | 0 to 1 |
| vibrant | prediction: virus | 1 |
| vibrant-virome | prediction: virus | 1 |
| virfinder | p-value: 0 to 1 | 0 to 1 |
| virnet | score: 0 to 1 | 0 to 1 |
| virsorter | category 1, category 2, category 3 | 1, 0.5, 0 |
| virsorter-virome | category 1, category 2, category 3 | 1, 0.5, 0 |
| virsorter2 | dsDNAphage: 0 to 1 | 0 to 1 |
# make sure that the fasta and .csv file are in the same directory
for i in bla ;
hier kommt noch was
oranage: #F79A30
pink #E35E9F
lila #8F2ABF
done
Tab. 1: Taxonomic classification of predicted phages based on sourmash using this database Each column can be filtered. The adjusted table can be exported as a .csv, .pdf or .excel.
hier nochn satz was der wert ist probability